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  <div class="section" id="compute-msd-command">
<span id="index-0"></span><h1>compute msd command<a class="headerlink" href="#compute-msd-command" title="Permalink to this headline">¶</a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID msd general_keyword general_values keyword values ...
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>msd = style name of this compute command</li>
<li>general_keywords general_values are documented in <a class="reference external" href="compute.html&quot;">compute</a></li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>com</em></li>
</ul>
<pre class="literal-block">
<em>com</em> value = <em>yes</em> or <em>no</em>
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all msd
compute 1 upper msd com yes
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Define a computation that calculates the mean-squared displacement
(MSD) of the group of atoms, including all effects due to atoms
passing thru periodic boundaries.  For computation of the non-Gaussian
parameter of mean-squared displacement, see the <a class="reference internal" href="compute_msd_nongauss.html"><em>compute msd/nongauss</em></a> command.</p>
<p>A vector of four quantites is calculated by this compute.  The first 3
elements of the vector are the squared dx,dy,dz displacements, summed
and averaged over atoms in the group.  The 4th element is the total
squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and
averaged over atoms in the group.</p>
<p>The slope of the mean-squared displacement (MSD) versus time is
proportional to the diffusion coefficient of the diffusing atoms.</p>
<p>The displacement of an atom is from its original position at the time
the compute command was issued.  The value of the displacement will be
0.0 for atoms not in the specified compute group.</p>
<p>If the <em>com</em> option is set to <em>yes</em> then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calcluated.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Initial coordinates are stored in &#8220;unwrapped&#8221; form, by
using the image flags associated with each atom.  See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command for a discussion of &#8220;unwrapped&#8221; coordinates.
See the Atoms section of the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a
discussion of image flags and how they are set for each atom.  You can
reset the image flags (e.g. to 0) before invoking this compute by
using the <a class="reference internal" href="set.html"><em>set image</em></a> command.</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If an atom is part of a rigid body (see the <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command), it&#8217;s periodic image flags are altered,
and its contribution to the MSD may not reflect its true contribution.
See the <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command for details.  Thus, to
compute the MSD of rigid bodies as they cross periodic boundaries, you
will need to post-process a <a class="reference internal" href="dump.html"><em>dump file</em></a> containing
coordinates of the atoms in the bodies.</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If you want the quantities calculated by this compute
to be continuous when running from a <a class="reference internal" href="read_restart.html"><em>restart file</em></a>,
then you should use the same ID for this compute, as in the original
run.  This is so that the created fix will also have the same ID, and
thus be initialized correctly with atom coordinates from the restart
file.</p>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global vector of length 4, which can be
accessed by indices 1-4 by any command that uses global vector values
from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-8"><span>this section</span></a> for an overview of LIGGGHTS(R)-PUBLIC output
options.</p>
<p>The vector values are &#8220;intensive&#8221;.  The vector values will be in
distance^2 <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
<p><a class="reference internal" href="compute_msd_nongauss.html"><em>compute msd/nongauss</em></a>, <a class="reference internal" href="compute_displace_atom.html"><em>compute displace_atom</em></a>, <a class="reference internal" href="fix_store_state.html"><em>fix store/state</em></a>, <a class="reference internal" href="compute_msd_molecule.html"><em>compute msd/molecule</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
<p>The option default is com = no.</p>
</div>
</div>


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